clusterSignifBase-class {goCluster} | R Documentation

## Class "clusterSignifBase"

### Description

This class provides a very simple selection mechanism to identify interesting annotation terms.

### Details

The class provides a wrapper around the `selectStats` function. Please read the corresponding documentation for further details.

### Slots

`threshold`:
  Object of class `"numeric"`, the threshold for selecting interesting annotation terms. This threshold is applied to the statistic returned by the `clusterStatistic`-class and any terms with a p-value lower than the threshold will be returned.

Additional slots are described in the documentation of the `clusterSignif-class` and `clusterModule-class`.

### Extends

Class `"clusterSignif"`, directly. Class `"clusterModule"`, by class `"clusterSignif"`.

### Methods

config
  `signature(object = "clusterSignifBase")`: interactive setup of the class. You can set the threshold here.
setup
  `signature(object = "clusterSignifBase")`: returns the configuration of the object as a list. This list can be used for the non-interactive setup of this class.
setup<-
  `signature(object = "clusterSignifBase")`: non-interactive setup of the class. You need to provide a list that contains the necessary settings for the class.
execute
  `signature(object = "clusterSignifBase")`: selects annotation terms that have a p-value lower than the given threshold.
reset
  `signature(object = "clusterSignifBase")`: resets the results of this class so that the selection process can be run again.
print
  `signature(object = "clusterSignifBase")`: This function prints some basic information about the content of this object. If the object has been executed, it will show the number of identified annotation terms.

### Author(s)

Gunnar Wrobel, http://www.gunnarwrobel.de.

### See Also

`selectStats`, `goCluster-class`, `clusterSignif-class`, `clusterModule-class`

### Examples

    ## Load a small test dataset
    data(benomylsetupsmall)

    ## Create an emty goCluster object
    test <- new("goCluster")

    ## Modify the configuration to use this significance class
    benomylsetupsmall$classsign <- "clusterSignifBase"

    ## Assign the configuration to the object and directly execute it
    execute(test) <- benomylsetupsmall

    ## This should show you the selected annotations. They should
    ## all have a value below 0.05.
    test@sign@selection

[Package goCluster version 1.0.3 Index]